You can only promote an Exchange organization to native mode if there are no servers running Exchange 5.5 (or earlier), and if no instances of Site Replication Service (SRS) are running. Also, make sure that you have correctly upgraded all servers and any connectors before you switch to native mode. After you switch an organization to native mode, it can never return to mixed mode. This means you cannot add an Exchange 5.5 server to a native mode topology.